I'm not sure if there is a workaround, but it sounds like there were some registry issues when you installed S7.
On the RSLogix 5000 side, what version of the software is installed? If it is the latest version (v. 13), then maybe the issue is caused by a conflict between the FactoryTalk components used by RSLogix and the registries S7 is attempting to modify.
I know that with other Rockwell software products, (RSView SE, for example) it must be installed first, and then other Rockwell products can be installed. Perhaps this is happening here, but in reverse (after all, I doubt Rockwell has considered testing the interaction of its software with a competing package).
If there are no obvious issues being caused by the registry errors, I would think everything is OK, and this may just be a nuisance (IMO). The only other thought that comes to mind would be to uninstall both SW packages and then reinstall S7 before RSLogix. But, as they say, "if it ain't broke, don't fix it!"
Regards,
Rick